Variety Of Side Chains Research Articles

Abstract 4033: A functional genome-wide screen to identify the ER degradation machinery in ER+ breast cancer cells

Abstract Targeted protein degradation (TPD) is a new pharmaceutical strategy to hijack the ubiquitin-proteasome system to degrade target proteins. Many TPD drugs are discovered serendipitously, and we are only beginning to harness their potential. Understanding how TPD drugs co-opt the proteolysis pathway is important, as it could allow molecule re-engineering for TPD of new proteins (ie. neo-substrates). A rising example of TPD drugs are the selective estrogen receptor degraders (SERDs) - small molecule antagonists of estrogen receptor alpha (ER) that target ER protein for degradation. SERDs are the next generation of therapy for metastatic ER+ breast cancer. Currently, fulvestrant is the only FDA approved SERD, but fulvestrant is limited by poor pharmacokinetics and resistance conferred by ER mutations (ie. ER-Y537S). An intense pharmaceutical effort has developed five novel SERDs in phase three clinical trials. These novel SERDs have diverse side chains for inducing ER degradation but share advantages including non-steroidal structure, oral bioavailability, and activity against ER-Y537. Based on the diverse molecular properties of SERDs, I hypothesized they utilize different ubiquitin-proteasome pathway genes (such as E3 ligases) for ER degradation. To identify the machinery for SERD-mediated ER degradation, I designed a functional CRISPR/Cas9 screen, with highlights including a genome-wide gRNA library and measurement of endogenous ER protein in ER+ breast cancer cells. Initially focusing on genes required for fulvestrant-mediated ER degradation, we identified the proteolysis pathway as a top hit (q<5x10-6) including central genes in the ubiquitin-proteasome pathway (UBC, PSMA6, and NEDD8) and the ubiquitin-like SUMO pathway (UBC9 and RWDD3). Ubiquitin E3 ligases were also identified, including FBXO45 and VHL, which have been previously implicated as E3 ligases for ER. These hits were validated using inhibitors of ubiquitin-, NEDD8-, and SUMO-activating enzymes. These results demonstrate that multiple proteolysis mechanisms are sufficient for ER protein degradation. Currently, I am applying this screening approach to novel SERDs (such as elacestrant, amnecestrant, and giredestrant) to identify overlapping and unique mechanisms of degradation for wild-type ER and ER-Y537S. Importantly, understanding the mechanisms of these exciting new drugs will allow anticipation of resistance mechanisms in advanced ER+ breast cancer patients. Citation Format: Zachary Sandusky. A functional genome-wide screen to identify the ER degradation machinery in ER+ breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4033.

Using automated synthesis to understand the role of side chains on molecular charge transport

The development of next-generation organic electronic materials critically relies on understanding structure-function relationships in conjugated polymers. However, unlocking the full potential of organic materials requires access to their vast chemical space while efficiently managing the large synthetic workload to survey new materials. In this work, we use automated synthesis to prepare a library of conjugated oligomers with systematically varied side chain composition followed by single-molecule characterization of charge transport. Our results show that molecular junctions with long alkyl side chains exhibit a concentration-dependent bimodal conductance with an unexpectedly high conductance state that arises due to surface adsorption and backbone planarization, which is supported by a series of control experiments using asymmetric, planarized, and sterically hindered molecules. Density functional theory simulations and experiments using different anchors and alkoxy side chains highlight the role of side chain chemistry on charge transport. Overall, this work opens new avenues for using automated synthesis for the development and understanding of organic electronic materials.

2-Methoxyethoxy functionalized triazine-cored conjugated polymers featuring hydrophilicity for enhanced visible-light photocatalytic degradation of antibiotic

Conjugated polymers (CPs) show enormous potential for photocatalytic degradation of antibiotics, but still exhibit unsatisfactory degradation rate due to the hydrophobicity. Herein, we report the designed synthesis of two visible-light-active triazine-cored CPs and their photocatalytic activities in tetracycline (TC) degradation. Interestingly, the hydrophilicity and opto-electronic properties of CPs can be readily tuned by selection of building blocks attached diverse side-chains. For CPs bearing photoactive center, the integration of 2-methoxyethoxy functional groups can prominently improve the hydrophilicity and reduce undesirable aggregation, which facilitates the adsorption of contaminants for the subsequent photodegradation reaction. Moreover, the embedded 2-methoxyethoxy moieties render the resulting CPs with narrower band gap, higher visible light-harvesting efficiency and charge carrier mobility, thus favoring the enhanced photocatalytic performance. As such, the CP involving 2-methoxyethoxy (BMTA-TAPT) has a higher photodegradation kinetic of TC, which is over 9 times the rate of the hydrophobic counterpart (TA-TAPT). The results provide a simple and effective approach for engineering high-performance polymer photocatalysts. • Visible-light-active triazine-cored CPs were designed and synthesized. • Introduction of 2-methoxyethoxy groups improved hydrophilicity, visible-light response ability and charge separation. • Hydrophilic BMTA-TAPT exhibited superior photocatalytic activity and stability. • Mechanism for photodegradation TC was elucidated.

Tuneable N‐Substituted Polyamides with High Biomass Content via Ugi 4 Component Polymerization

AbstractUgi 4‐component reaction (Ugi 4CR) is an efficient tool which benefits from high atom efficiency, compatibility with green solvents such as methanol, simple purification, and a water side‐product. By using two bifunctional starting materials for Ugi 4CR, N‐substituted polyamides can be prepared via a step‐growth process. As polyamides play important roles in applications including films, and adhesives, the preparation of N‐substituted functional polyamides from largely sustainable monomers is investigated. Herein, the combination of renewable diamine, diacid, and aldehydes with commercially available isocyanides yield polyamides with tuneable side chain functionalities and ≈80% biomass content. Relatively high yields (up to 96%) are recorded for polymers of moderate molecular weights (Mw up to 8100 g mol−1). The prepared polyamides possess backbones which exhibit excellent thermal stability (Tdeg = 440 ± 10 °C), while functional side chains result in additional lower‐temperature degradations (215–285 °C). Side‐group variation enables shifting of the glass transition temperature (Tg) between 9 and 38 °C and causes variation in hydrophobicity resulting in water contact angles ranging from 47 o to 105 o. This work presents a reliable approach to prepare sustainable polymers with diverse side chain functionalities in a short reaction time and without need for catalysts or complicated purifications.

Systematic investigation of the influence of electronic substituents on dinuclear gold(I) amidinates: synthesis, characterisation and photoluminescence studies.

Dinuclear gold(I) compounds are of great interest due to their aurophilic interactions that influence their photophysical properties. Herein, we showcase that gold-gold interactions can be influenced by tuning the electronic properties of the ligands. Therefore, various para substituted (R) N,N'-bis(2,6-dimethylphenyl)formamidinate ligands (pRXylForm; Xyl = 2,6-dimethylphenyl and Form = formamidinate) were treated with Au(tht)Cl (tht = tetrahydrothiophene) to give via salt metathesis the corresponding gold(I) compounds [pRXylForm2Au2] (R = -OMe, -Me, -Ph, -H, -SMe, and -CO2Me). All complexes showed intense luminescence properties at low temperatures. Alignment with the Hammett parameter σp revealed the trends in the 1H and 13C NMR spectra. These results showed the influence of the donor-acceptor abilities of different substituents on the ligand system which were confirmed with calculated orbital energies. Photophysical investigations showed their lifetimes in the millisecond range indicating phosphorescence processes and revealed a redshift with the decreasing donor ability of the substituents in the solid state.

Impact of varying side chain structure on organic electrochemical transistor performance: a series of oligoethylene glycol-substituted polythiophenes

We find larger μC* and faster doping kinetics with more oxygen atoms on the side chain, and if the oxygen atom is farther from the polymer backbone. We show that this variation in C* is the dominant factor in changing the μC* for these polymers.

Polypeptoids and Peptoid-Peptide Hybrids by Transition Metal Catalysis.

Peptoids have attracted attention for application in biomedicine due to their advantageous properties as compared to peptides. The structural analogues are typically resistant to protease degradation and offer improved biocompatibility. Chemical routes to an impressive variety of short-chain, low-molecular-weight peptoids are well-established. However, synthetic methods for well-defined, high-molecular-weight polypeptoids with side chain diversity are still in their infancy. Here, we report a facile method for synthesis of polypeptoids via transition-metal-catalyzed controlled, living polymerization of N-substituted N-carboxyanhydrides. Our method is amenable to hydrophilic and hydrophobic side chains and yields high-molecular-weight linear polypeptoids of predictable length and low dispersity. Further, the polymer end groups can be tuned for biological targeting, and polypeptide-polypeptoid hybrids are readily prepared in one pot. Our materials are indeed resistant to common proteases and are well-tolerated by human cells. Overall, this work represents a significant stride toward access to tunable polypeptoids.

Self-healing antifouling polymer brushes: Effects of degree of fluorination

Heavily fluorinated polymeric coatings are used by industry in the prevention of polymeric fouling. However, due to their potential toxicity and lack of durability, there is an increasing demand for sustainable alternatives. In this research, eleven polymer brushes with varying side chain lengths and degrees of fluorination have been developed, and their antifouling and self-healing performances have been compared. In all cases where damage was inflicted by a pH 3 solution, the coatings – including the non-fluorinated ones – showed full restoration of their contact angle upon placement in an oven at 120 °C, confirming the self-healing ability of this range of coatings. One coating, poly(C10-MAF0), was unharmed by the acidic conditions, hence no self-healing capability could be established. Investigation with four fluorescently labelled polymer solutions and confocal fluorescent microscopy confirmed that all coatings have antifouling properties towards organic polymers. The more heavily fluorinated polymer brushes performed better than the rest, and not the non-fluorinated but rather the singly fluorinated brushes showed the least antifouling capability. Determination of the critical surface tension confirmed this trend: the heavily fluorinated polymer brushes have the lowest critical surface tension, and the singly fluorinated polymer brushes have the highest. A lack of alignment of the side chains of the polymer brushes is the proposed reason for this, explaining the contrast with previously reported monolayer experiments. Finally, we explain why both fluorinated and non-fluorinated brushes display self-healing characteristics.

Notoginsenoids, a new class of hexa-nortriterpenoids from biotransformation of Panax notoginseng saponins

Notoginsenoids T1−T7, a new class of hexa-nortriterpenoids including two dimers and five monomers, possessing an unprecedented 9-en-5-ketone tricyclic hexa-nordammar skeleton and a variable side chain at C-17, were obtained from biotransformation of PPD-type dammarane saponins by the soil harvested with Panax notoginseng (Araliaceae), a famous traditional Chinese medicinal herb. Their structures were unambiguously determined by spectroscopic, single-crystal X-ray diffraction, Mo2(AcO)4-induced CD and ECD analyzes. A plausible biotransformed pathway for T1−T7 was proposed. Notoginsenoids T1−T5 showed growth inhibitory effects on the probiotic and pathogenic fungi of P. notoginseng.

Synthesis and Evaluation of Quinone Derivatives for Activity against Trypanosome cruzi.

A series of quinone derivatives with a variety of side chains were synthesized. These synthetic quinone compounds were evaluated for in vitro antitrypanosomal activity against trypomastigotes and amastigotes of Trypanosoma cruzi, the causative agent of Chagas disease. Measurement of solubility of quinones and their ability to permeate cell membranes were assessed to address their possible use as oral drugs. Some synthesized compounds exhibited potent antitrypanosomal activity. However, most compounds with a promising activity showed poor solubility that did not seem suitable for oral usage. Meanwhile, compound 5a, an N-tert-butoxycarbonylpiperidine derivative, exhibited good antitrypanosomal activity, ability to permeate membranes, and good solubility.

Synthesis and biological evaluation of BU-4664L derivatives as potential anticancer agents

BU-4664L is a naturally occurring N-farnesylated dibenzodiazepinone with important biological activities. Herein, we report the synthesis and antitumor evaluation of two series of BU-4664L derivatives bearing different substituent patterns on the dibenzodiazepinone core and with diverse side chains. All of the derivatives displayed micromolar activity against the human prostate cancer PC-3 cells, while lower or no activity against the human lung H460 cells. The most active derivatives were 10a and 16c which exerted antiproliferative activity against PC-3 cells with GI50 values of 5.66 and 5.94 μM, respectively, and thus represent promising lead compounds for further development.

Systematic Investigation of Solution-State Aggregation Effect on Electrical Conductivity in Doped Conjugated Polymers

Systematic Investigation of Solution-State Aggregation Effect on Electrical Conductivity in Doped Conjugated Polymers

Thermal and Barrier Characterizations of Cellulose Esters with Variable Side-Chain Lengths and Their Effect on PHBV and PLA Bioplastic Film Properties.

Cellulose esters (CEs) are promising biodegradable substitutes for traditional petroleum-based plastic materials. Research on structure–property relationships of CEs is necessary to evaluate their suitability for industrial applications such as food packaging. Cellulose esters with different side-chain lengths were synthesized and studied. Their thermal and moisture barrier properties were characterized. Cellulose triheptanoate (CTH) was proved to have an optimal moisture barrier (WVTR = 0.31 g·mil/day/in.2) and was used to blend with poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and polylactic acid (PLA) bioplastics. CTH addition improved the PLA thermal stability, enhanced the ductility, and increased the moisture barrier by 32%, while it decreased the PHBV thermal stability, weakened the ductility, and reduced the moisture barrier by 90%. We demonstrated that by proper choice of the combination of CE and bioplastic, bioplastic blends with unique and useful synergistic properties can be obtained. These blends can potentially be used for commercial applications, such as biodegradable flexible packaging.

High Yields of Aromatic Monomers from Acidolytic Oxidation of Kraft Lignin in a Biphasic System

In this work, acidic oxidation in a biphasic water/octanol system was applied to mitigate condensation and increase the yields of high-value aromatic monomers from Kraft lignin, a waste product, and an industrially relevant feedstock. Biphasic depolymerization (BPD) is a one-pot multistep technique in which target molecules are protected from degradation in the reactive aqueous milieu (necessary for the cleavage of β-O-4 bonds as well as the recalcitrant high dissociation energy carbon–carbon moieties) by an in situ transfer of the products into the protective octanol phase. The results have shown overall monomeric yields up to 13 wt % and yields of vanillin up to 7 wt % (FeCl3 as a catalyst and O2 as an oxidant), significantly outperforming the previously reported monophasic and biphasic outcomes for Kraft lignin. In addition to increased yields, BPD also resulted in an expansion of the product pool from few molecules typically reported in the literature to 64 aromatic monomers detected at various concentration levels in the current work. The identified aromatic alcohols, carbonyl compounds, and carboxylic acids incorporating varying side chain lengths show potential as green and sustainable replacements to BTX (benzene, toluene, and xylene) petrochemicals. BPD as a process coupled mild conversion conditions, cheap oxidants, and common homogeneous catalysts with an in situ separation of the products from the reaction mixture to yield excellent results in converting industrial waste and recalcitrant feedstocks into value.

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices.

As the only ribosomally encoded N-substituted amino acid, proline promotes distinct secondary protein structures. The high proline content in collagen, the most abundant protein in the human body, is crucial to forming its hallmark structure: the triple-helix. For over five decades, proline has been considered compulsory for synthetic designs aimed at recapitulating collagen's structure and properties. Here we describe that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, enabling synthesis of stable triple-helical collagen mimetic peptides (CMPs) with unprecedented side chain diversity. Supported by atomic-resolution crystal structures as well as circular dichroism and computational characterizations spanning over 30 N-gly-containing CMPs, we discovered that N-glys stabilize the triple-helix primarily by sterically preorganizing individual chains into the polyproline-II helix. We demonstrated that N-glys with exotic side chains including a "click"-able alkyne and a photosensitive side chain enable CMPs for functional applications including the spatiotemporal control of cell adhesion and migration. The structural principles uncovered in this study open up opportunities for a new generation of collagen-mimetic therapeutics and materials.

Nucleic Acid Delivery across Biological Barriers

One of the current critical issues in nucleic acid delivery is the efficient mRNA delivery into target cells, directed toward clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genome editing. To this end, we have developed a variety of cationic polyaspartamide derivatives with varying side chain structures because they can form nanocomplexes, termed polyplexes, with mRNA through electrostatic interactions. Interestingly, the delivery functions were highly affected by the chemical structures of the polyaspartamide side chains. Therefore, we review our previous research and provide a rationale for designing polypeptides for mRNA delivery.

Easily Functionalized and Readable Sequence-Defined Polytriazoles.

Developing sequence-defined skeletons that could be conveniently characterized and functionalized with diverse side groups is attractive but challenging. Here we report one novel sequence-defined polytriazole structure bearing side groups at its triazole rings. Its construction was facilely accessed by the iterative employments of azidation and iridium-catalyzed cycloaddition of azide with internal 1-thioalkyne (IrAAC) in solution phase. The easy preparation of 1-thioalkyne monomers and the excellent tolerance of IrAAC enable the introduction of diverse functional side chains to this architecture. The obtained sequence was effectively characterized by tandem mass spectrometry owing to the efficient fractures of both of the Csp3-S and Csp3-N bonds in its backbone, indicating its potential utilization in high-capacity digital polymer developments. Further successful application of this structure in building monodisperse macromolecules exhibiting aggregation-induced emission (AIE) characteristics demonstrates its expected application in functional material fabrications.

Bioinspired Brønsted Acid-Promoted Regioselective Tryptophan Isoprenylations.

Tryptophan-containing isoprenoid indole alkaloid natural products are well known for their intricate structural architectures and significant biological activities. Nature employs dimethylallyl tryptophan synthases (DMATSs) or aromatic indole prenyltransferases (iPTs) to catalyze regio- and stereoselective prenylation of l-Trp. Regioselective synthetic routes that isoprenylate cyclo-Trp-Trp in a 2,5-diketopiperazine (DKP) core, in a desymmetrizing manner, are nonexistent and are highly desirable. Herein, we present an elaborate report on Brønsted acid-promoted regioselective tryptophan isoprenylation strategy, applicable to both the monomeric amino acid and its dimeric l-Trp DKP. This report outlines a method that regio- and stereoselectively increases sp3 centers of a privileged bioactive core. We report on conditions involving screening of Brønsted acids, their conjugate base as salt, solvent, temperature, and various substrates with diverse side chains. Furthermore, we extensively delineate effects on regio- and stereoselection of isoprenylation and their stereochemical confirmation via NMR experiments. Regioselectively, the C3-position undergoes normal-isoprenylation or benzylation and forms exo-ring-fused pyrroloindolines selectively. Through appropriate prenyl group migrations, we report access to the bioactive tryprostatin alkaloids, and by C3-normal-farnesylation, we access anticancer drimentines as direct targets of this method. The optimized strategy affords iso-tryprostatin B-type products and predrimentine C with 58 and 55% yields, respectively. The current work has several similarities to biosynthesis, such as—reactions can be performed on unprotected substrates, conditions that enable Brønsted acid promotion, and they are easy to perform under ambient conditions, without the need for stoichiometric levels of any transition metal or expensive ligands.

Poly(2-ethyl-2-oxazoline) bottlebrushes: How nanomaterial dimensions can influence biological interactions

Biocompatible polymers are crucial components of successful nano-sized carriers, which enable the delivery of otherwise largely ineffective therapeutics. Poly(2-ethyl-2-oxazoline) (PEtOx) is one polymer that has shown potential for this application due to its demonstrated low fouling nature and biocompatibility comparable to the current gold standard carrier, poly(ethylene glycol). PEtOx based bottlebrushes, in particular, are promising therapeutic carriers due to their anisotropic nature, which can be easily fine-tuned. Despite this potential, little is known about the interaction of PEtOx bottlebrushes with biological systems. The present study provides a detailed insight into the cellular interactions and biodistribution of PEtOx bottlebrushes in a mouse model. Three PEtOx bottlebrushes of varied side-chain and backbone lengths were designed to highlight the effect that the degree of polymerisation (DP) of each aspect may have on both cellular interaction and biodistribution. Herein we show that PEtOx bottlebrushes display no adverse effects to either cells or mice over 48 h at doses that would be relevant to drug delivery applications. Furthermore, increasing either the backbone or side-chain length of PEtOx bottlebrushes leads to a reduction in cellular association in vitro and an increase in blood circulation times in vivo. The fact that small changes to the dimensions of the PEtOx bottlebrushes have a marked effect on biodistribution and blood circulation times may prove to be a highly beneficial insight for the design of next-generation PEtOx bottlebrushes nanocarriers with tailor-made profiles dependent on the application required.

Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure.

Advances in the design of permeable peptides and in the synthesis of large arrays of macrocyclic peptides with diverse amino acids have evolved on parallel but independent tracks. Less precedent combines their respective attributes, thereby limiting the potential to identify permeable peptide ligands for key targets. Herein, we present novel 6-, 7-, and 8-mer cyclic peptides (MW 774-1076 g·mol-1) with passive permeability and oral exposure that feature the amino acids and thioether ring-closing common to large array formats, including DNA- and RNA-templated synthesis. Each oral peptide herein, selected from virtual libraries of partially N-methylated peptides using in silico methods, reflects the subset consistent with low energy conformations, low desolvation penalties, and passive permeability. We envision that, by retaining the backbone N-methylation pattern and consequent bias toward permeability, one can generate large peptide arrays with sufficient side chain diversity to identify permeability-biased ligands to a variety of protein targets.